Variant report

Variant	rs4672040
Chromosome Location	chr2:55640649-55640650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55626650..55628970-chr2:55639819..55642299,2	K562	blood:
2	chr2:55633136..55639027-chr2:55639441..55643745,9	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10169185	0.94[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10184756	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11125568	0.85[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125569	1.00[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125572	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11695152	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12617891	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs12618216	0.90[ASN][1000 genomes]
rs12618795	0.85[JPT][hapmap]
rs12623954	0.98[ASN][1000 genomes]
rs12713297	0.84[ASN][1000 genomes]
rs13008631	0.86[AFR][1000 genomes]
rs1454415	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454419	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1454420	0.98[ASN][1000 genomes]
rs1454423	0.98[ASN][1000 genomes]
rs1454424	0.98[ASN][1000 genomes]
rs1545554	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs1598163	0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap]
rs1902057	0.94[GIH][hapmap];0.81[TSI][hapmap]
rs1902061	1.00[CEU][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1902062	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2045134	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045135	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045136	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2123983	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs2219130	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2867178	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2867179	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2867194	0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs2903509	0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2903514	1.00[ASN][1000 genomes]
rs2966466	0.86[CEU][hapmap]
rs3099080	0.80[GIH][hapmap];0.81[TSI][hapmap]
rs3748943	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3762511	0.98[ASN][1000 genomes]
rs4233961	0.88[GIH][hapmap];0.87[JPT][hapmap]
rs4277563	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4484068	0.86[MEX][hapmap]
rs4672034	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672035	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4672037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4672038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4672041	0.98[ASN][1000 genomes]
rs4672043	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4672044	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4672045	0.94[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56201519	0.93[AFR][1000 genomes]
rs58708869	0.93[AFR][1000 genomes]
rs6545489	0.85[JPT][hapmap]
rs6545490	0.91[GIH][hapmap];0.87[JPT][hapmap]
rs6545491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6545492	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705104	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6709204	1.00[ASW][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6720698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721593	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6724840	0.85[JPT][hapmap]
rs6732633	0.91[ASN][1000 genomes]
rs6732759	0.99[ASN][1000 genomes]
rs6733814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744426	0.92[ASN][1000 genomes]
rs6748979	0.98[ASN][1000 genomes]
rs7424286	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7559987	1.00[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7574743	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7579037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586440	0.85[JPT][hapmap]
rs7589279	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7601588	0.88[GIH][hapmap]
rs7602189	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603105	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7606361	0.80[GIH][hapmap];0.81[TSI][hapmap]
rs9751964	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4672040	FLJ31438	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
3	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
4	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
7	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
8	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
9	chr2:55624400-55645600	Weak transcription	Ovary	ovary
10	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
11	chr2:55630400-55645800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:55630600-55644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:55630800-55642400	Weak transcription	Pancreas	Pancrea
14	chr2:55630800-55644800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:55630800-55645200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:55630800-55645200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:55631000-55645400	Weak transcription	Placenta	Placenta
18	chr2:55631200-55642600	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:55631400-55642600	Weak transcription	Right Ventricle	heart
20	chr2:55631800-55645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:55632000-55644800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:55632600-55645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:55632800-55645800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:55633000-55645000	Weak transcription	Liver	Liver
25	chr2:55633000-55645800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:55633000-55645800	Weak transcription	Spleen	Spleen
27	chr2:55633000-55646000	Weak transcription	Lung	lung
28	chr2:55633200-55644800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:55636200-55644200	Weak transcription	Fetal Heart	heart
30	chr2:55636400-55642400	Weak transcription	Fetal Brain Female	brain
31	chr2:55636400-55642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:55636600-55641000	Strong transcription	Fetal Thymus	thymus
33	chr2:55636600-55643200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:55636600-55644000	Weak transcription	HSMMtube	muscle
35	chr2:55636800-55642200	Weak transcription	NHLF	lung
36	chr2:55636800-55642600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:55636800-55642800	Weak transcription	NH-A	brain
38	chr2:55636800-55644000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:55636800-55644000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:55636800-55644000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:55636800-55644400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:55636800-55645600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:55637000-55641000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr2:55637000-55641800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:55637200-55641000	Strong transcription	Thymus	Thymus
46	chr2:55637200-55641200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:55637200-55642200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:55637400-55641400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:55637400-55644600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr2:55637400-55645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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